To reproduce (tested on a Marshmallow device):

1. On device A, navigate to facebook.com (or any site which has a custom web app manifest).

2. Choose "add to homescreen" from the menu.

3. On device B, perform a factory reset and restore Android backup data during the setup phase.

4. The homescreen shortcut is restored, but clicking on it opens Facebook as a tab in Chrome instead of a fullscreen activity. That is, the web app manifest wasn't restored during the backup.